" The three axle trucks with three core holes in the frames between the pedestals... " You are referring to the standard EMD Dash 2 truck. Curiously, Conrail specified the non - Dash 2 HD truck on their SD - 40 - 2's built new. This truck is often referred to as a 'HT-C', though I've seen the same reference used for the original EMD SD locomotive truck.
" The ones with two holes have even spaced axles ..." This was the EMD standard SD truck, also referred to as 'HD'. This truck was standard on all EMD SD - series units, with some modification to brake rigging & cylinders.
Note that both trucks have a slight offset in the axle spacing; the HT-C differed in having an outside hung traction motor on one end to allow all motors on a truck to face the same way. The HT-C truck offered an 12% increase in tractive effort vs. the original HD truck. Unfortunately the two trucks are not interchangeable due to the center plate having a different diameter. In other words you cannot simply place Dash 2 trucks under an older SD Locomotive to improve the T.E., as it would require replacing the frame member holding the center plate.
Joe Strapac's Southern Pacific Historic Diesels - Volume # 12 & 14, cover the subject very well.